Contrastingly, sometimes we might also use genetic information to do the exact opposite. While so many species on Earth are at risk (or have already passed over the precipice) of extinction, some have gone rogue with our intervention. These are, of course, invasive species; pests that have been introduced into new environments and, by their prolific nature, start to throw out the balance of the ecosystem. Australians will be familiar with no shortage of relevant invasive species; the most notable of which is the cane toad, Rhinella marina. However, there are a plethora of invasive species which range from notably prolific (such as the cane toad) to the seemingly mundane (such as the blackbird): so how can we possibly deal with the number and propensity of pests?
Tools for invasive species management
There are a number of tools at our disposal for dealing with invasive species. These range from chemical controls (like pesticides), to biological controls and more recently to targeted genetic methods. Let’s take a quick foray into some of these different methods and their applications to pest control.
The potential secondary impact of biological controls, and the degree of unpredictability in how they will respond to a new environment (and how native species will also respond to their introduction) leads conservationists to develop new, more specific techniques. In similar ways, viral and bacterial-based controls have had limited success (although are still often proposed in conservation management, such as the planned carp herpesvirus release).
The better we understand invasive species and populations from a genetic perspective, the more informed our management efforts can be and the more likely we are to be able to adequately address the problem.
Managing invasive pest species
The impact of human settlement into new environments is exponentially beyond our direct influences. With our arrival, particularly in the last few hundred years, human migration has been an effective conduit for the spread of ecologically-disastrous species which undermine the health and stability of ecosystems around the globe. As such, it is our responsibility to Earth to attempt to address our problems: new genetic techniques is but one growing avenue by which we might be able to remove these invasive pests.
Note: For some clear, interesting presentations on the topic of de-extinction, and where some of the information for this post comes from, check out this list of TED talks.
The current conservation crisis
The stark reality of conservation in the modern era epitomises the crisis disciplinethat so often is used to describe it: species are disappearing at an unprecedented rate, and despite our best efforts it appears that they will continue to do so. The magnitude and complexity of our impacts on the environment effectively decimates entire ecosystems (and indeed, the entire biosphere). It is thus our responsibility as ‘custodians of the planet’ (although if I had a choice, I would have sacked us as CEOs of this whole business) to attempt to prevent further extinction of our planet’s biodiversity.
There’s one catch (well, a few really) with genetic rescue: namely, that one must have other populations to ‘outbreed’ with in order add genetic variation to the captive population. But what happens if we’re too late? What if there are no other populations to supplement with, or those other populations are also too genetically depauperate to use for genetic rescue?
Believe it or not, sometimes it’s not too late to save species, even after they have gone extinct. Which brings us from this (lengthy) introduction to this week’s topic: de-extinction. Yes, we’re literally (okay, maybe not) going to raise the dead.
Backbreeding: resurrection by hybridisation
You might wonder how (or even if!) this is possible. And to be frank, it’s extraordinarily difficult. However, it has to a degree been done before, in very specific circumstances. One scenario is based on breeding out a species back into existence: sometimes we refer to this as ‘backbreeding’.
This practice really only applies in a few select scenarios. One requirement for backbreeding to be possible is that hybridisation across species has to have occurred in the past, and generally to a substantial scale. This is important as it allows the genetic variation which defines one of those species to live on within the genome of its sister species even when the original ‘host’ species goes extinct. That might make absolutely zero sense as it stands, so let’s dive into this with a case study.
One of these species, Chelonoidis elephantopus, also known as the Floreana tortoise after their home island, went extinct over 150years ago, likely due to hunting and trade. However, before they all died, some individuals were transported to another island (ironically, likely by mariners) and did the dirty with another species of tortoise: C. becki. Because of this, some of the genetic material of the extinct Floreana tortoiseintrogressed into the genome of the still-living C. becki. In an effort to restore an iconic species, scientists from a number of institutions attempted to do what sounds like science-fiction: breed the extinct tortoise back to life.
When you saw the title for this post, you were probably expecting some Jurassic Parklevel ‘dinosaurs walking on Earth again’ information. I know I did when I first heard the term de-extinction. Unfortunately, contemporary de-extinction practices are not that far advanced just yet, although there have been some solid attempts. Experiments conducted using the genomic DNA from the nucleus of a dead animal, and cloning it within the egg of another living member of that species has effectively cloned an animal back from the dead. This method, however, is currently limited to animals that have died recently, as the DNA degrades beyond use over time.
One might expect that as genomic technologies improve, particularly methods facilitated by the genome-editing allowed from CRISPR/Cas-9 development, that we might one day be able to truly resurrect an extinct species. But this leads to very strongly debated topics of ethics and morality of de-extinction. If we can bring a species back from the dead, should we? What are the unexpected impacts of its revival? How will we prevent history from repeating itself, and the species simply going back extinct? In a rapidly changing world, how can we account for the differences in environment between when the species was alive and now?
There is no clear, simple answer to many of these questions. We are only scratching the surface of the possibility of de-extinction, and I expect that this debate will only accelerate with the research. One thing remains eternally true, though: it is still the distinct responsibility of humanity to prevent more extinctions in the future. Handling the growing climate change problem and the collapse of ecosystems remains a top priority for conservation science, and without a solution there will be no stable planet on which to de-extinct species.
Divisiveness is becoming quickly apparent as a plague on the modern era. The segregation and categorisation of people – whether politically, spiritually or morally justified – permeates throughout the human condition and in how we process the enormity of the Homo sapien population. The idea that the antithetic extremes form two discrete categories (for example, the waning centrist between ‘left’ vs. ‘right’ political perspectives) is widely employed in many aspects of the world.
But how pervasive is this pattern? How well can we summarise, divide and categorise people? For some things, this would appear innately very easy to do – one of the most commonly evoked divisions in people is that between men and women. But the increasingly charged debate around concepts of both gender and sex (and sexuality as a derivative, somewhat interrelated concept) highlights the inconsistency of this divide.
The ‘sex’ and ‘gender’ arguments
The most commonly used argument against ‘alternative’ concepts of either gender of sex – the binary states of a ‘man’ with a ‘male’ body and a ‘female’ with a ‘female’ body – is often based on some perception of “biologically reality.” As a (trainee) biologist, let me make this apparently clear that such confidence and clarity of “reality” in many, if not all, biological subdisciplines is absurd (e.g. “nature vs. nurture”). Biologists commonly acknowledge (and rely upon) the realisation that life in all of its constructs is unfathomably diverse, unique, and often difficult to categorise. Any impression of being able to do so is a part of the human limitation to process concepts without boundaries.
As an extension of the gender debate, sex itself has often been relied upon as the last vestige of some kind of sexual binary. Even for those more supported of trans people, sex is often described as some concrete, biologically, genetically-encoded trait which conveniently falls into its own binary system. Thus, instead of a single binary, people are reduced down to a two-character matrix of sex and gender.
You might be under the impression that these are rare ‘genetic disorders’, and don’t count as “real people” (decidedly not my words). But the reality is that intersex people are relatively common throughout the world, and occur roughly as frequently as true redheads or green eyes. Thus, the idea that excluding intersex people from the rest of societal definitions has very little merit, especially from a scientific point of view. Instead, allowing our definitions of both sex and gender to be broad and flexible allows us to incorporate the biological reality of the immense diversity of the world, even just within our own species.
Anyone who argues a biological basis for these concepts is taking the good name of biological science hostage. Diversity underpins the most core aspects of biology (e.g. evolution, communities and ecosystems, medicine) and is a real attribute of living in a complicated world. Downscaling and simplifying the world to the ‘black’ and the ‘white’ discredits the wonder of biology, and acknowledging the ‘outliers’ (especially those that are not actually so far outside the boxes we have drawn) of any trends we may observe in nature is important to understand the complexity of life on Earth. Even if individual components of this post seem debatable to you: always remember that life is infinitely more complex and colourful than we can even imagine, and all of that is underpinned by diversity in one form or another.
To expand on this, we’re going to look at a few different models of how the spatial distribution of populations influences their divergence, and particularly how these factor into different processes of speciation.
What comes first, ecological or genetic divergence?
The order of these two processes have been in debate for some time, and different aspects of species and the environment can influence how (or if) these processes occur.
Different spatial models of speciation
Generally, when we consider the spatial models for speciation we divide these into distinct categories based on the physical distance of populations from one another. Although there is naturally a lot of grey area (as there is with almost everything in biological science), these broad concepts help us to define and determine how speciation is occurring in the wild.
A step closer in bringing populations geographically together in speciation is “parapatry” and “peripatry”. Parapatric populations are often geographically close together but not overlapping: generally, the edges of their distributions are touching but do not overlap one another. A good analogy would be to think of countries that share a common border. Parapatry can occur when a species is distributed across a broad area, but some form of narrow barrier cleaves the distribution in two: this can be the case across particular environmental gradients where two extremes are preferred over the middle.
This can be tricky to visualise, so let’s invent an example. Say we have a tropical island, which is occupied by one bird species. This bird prefers to eat the large native fruit of the island, although there is another fruit tree which produces smaller fruits. However, there’s only so much space and eventually there are too many birds for the number of large fruit trees available. So, some birds are pushed to eat the smaller fruit, and adapt to a different diet, changing physiology over time to better acquire their new food and obtain nutrients. This shift in ecological niche causes the two populations to become genetically separated as small-fruit-eating-birds interact more with other small-fruit-eating-birds than large-fruit-eating-birds. Over time, these divergences in genetics and ecology causes the two populations to form reproductively isolated species despite occupying the same island.
As you can see, the processes and context driving speciation are complex to unravel and many factors play a role in the transition from population to species. Understanding the factors that drive the formation of new species is critical to understanding not just how evolution works, but also in how new diversity is generated and maintained across the globe (and how that might change in the future).
Like many people, from a young age I was obsessed and interested in works of fantasy and science fiction. To feel transported to magical worlds of various imaginative creatures and diverse places. The luxury of being able to separate from the mundanity of reality is one many children (or nostalgic adults) will be able to relate to upon reflection. Worlds that appear far more creative and engaging than our own are intrinsically enticing to the human psyche and the escapism it allows is no doubt an integral part of growing up for many people (especially those who have also dealt or avoided dealing with mental health issues).
The intricate connection to the (super)natural world drove me to fall in love with the natural world. Although there might seem to be an intrinsic contrast between the two – the absence or presence of reality – the truth is that the world is a wondrous place if you observe it through an appropriate lens. Dragons are real, forms of life are astronomically varied and imaginative, and there we are surrounded by the unknown and potentially mythical. To see the awe and mystification on a child’s face when they see a strange or unique animal for the very first time bears remarkable parallels to the expression when we stare into the fantasy of Avatar or The Lord of the Rings.
It might seem common for ‘nerds’ (at least under the traditional definition of being obsessed with particular aspects of pop culture) to later become scientists of some form or another. And I think this is a true reflection: particularly, I think the innate personality traits that cause one to look at the world of fantasy with wonder and amazement also commonly elicits a similar response in terms of the natural world. It is hard to see an example where the CGI’d majesty of contemporary fantasy and sci-fi could outcompete the intrigue generated by real, wondrous plants and animals.
Seeing the divine in the mundane
Although we often require a more tangible, objective justification for research, the connection of people to the diversity of life (whether said diversity is fictitious or not) should be a significant driving factor in the perceived importance of conservation management. However, we are often degraded to somewhat trivial discussions: why should we care about (x) species? What do they do for us? Why are they important?
If we approach the real world and the organisms that inhabit it with truly the same wonder as we approach the fantastical, would we be more successful in preserving biodiversity? Could we reverse our horrific trend of letting species go extinct? Every species on Earth represents something unique: a new perspective, an evolutionary innovation, a lens through which to see the world and its history. Even the most ‘mundane’ of species represent something critical to functionality of ecosystems, and their lack of emphasis undermines their importance.
The biota of Earth are no different to the magical fabled beasts of science fiction and fantasy, and we’re watching it all burn away right in front of our eyes.
The first major component that is needed for SDM is the occurrence data. Some methods will work with presence-only data: that is, a map of GPS coordinates which describes where that species has been found. Others work with presence-absence data, which may require including sites of known non-occurrence. This is an important aspect as the non-occurring sites defines the environment beyond the tolerance threshold of the species: however, it’s very likely that we haven’t sampled every location where they occur, and there will be some GPS co-ordinates that appear to be absent of our species where they actually occur. There are some different analytical techniques which can account for uneven sampling across the real distribution of the species, but they can get very technical.
Our SDM analysis of choice (e.g. MaxEnt) will then use various algorithms to build a model which best correlates where the species occurs with the environmental variables at those sites. The model tries to create a set of environmental conditions that best encapsulate the occurrence sites whilst excluding the non-occurrence sites from the prediction. From the final model, we can evaluate how strong the effect of each of our variables is on the distribution of the species, and also how well our overall model predicts the locality data.
Species distribution modelling continues to be a useful tool for conservation and evolution studies, and improvements in analytical algorithms, available environmental data and increased sampling of species will similarly improve SDM. Particularly, improvements in environmental projections from both the distant past and future will improve our ability to understand and predict how species will change, and have changed, with climatic changes
This is Part 1 of a four part miniseries on the process of speciation; how we get new species, how we can see this in action, and the end results of the process. This week, we’ll start with a seemingly obvious question: what is a species?
The definition of a ‘species’
‘Species’ are a human definition of the diversity of life. When we talk about the diversity of life, and the myriad of creatures and plants on Earth, we often talk about species diversity. This might seem glaringly obvious, but there’s one key issue: what is a species, anyway? While we might like to think of them as discrete and obvious groups (a dog is definitely not the same species as a cat, for example), the concept of a singular “species” is actually the result of human categorisation.
In reality, the diversity of life is spread across a huge spectrum of differentiation: from things which are closely related but still different to us (like chimps), to more different again (other mammals), to hardly relatable at all (bacteria and plants). So, what is the cut-off for calling something a species, and not a different genus, family, or kingdom? Or alternatively, at what point do we call a specific sub-group of a species as a sub-species, or another species entirely?
This might seem like a simple question: we look at two things, and they look different, so they must be different species, right? Well, of course, nature is never simple, and the line between “different” and “not different” is very blurry. Here’s an example: consider that you knew nothing about the history, behaviour or genetics of dogs. If you simply looked at all the different breeds of dogs on Earth, you might suggest that there are hundreds of species of domestic dogs. That seems a little excessive though, right? In fact, the domestic dog, Eurasian wolf, and the Australian dingo are all the same species (but different subspecies, along with about 38 others…but that’s another issue altogether).
For example, a horse and zebra can breed to produce a zorse, however zorse are fundamentally infertile (due to the different number of chromosomes between a horse and a zebra) and thus a horse is a different species to a zebra. However, a German Shepherd and a chihuahua can breed and make a hybrid mutt, so they are the same species.
To try and account for the issues with the BSC, taxonomists try to push for the usage of “integrative taxonomy”. This means that species should be defined by multiple different agreeing concepts, such as reproductive isolation, genetic differentiation, behavioural differences, and/or ecological traits. The more traits that can separate the two, the greater support there is for the species to be separated: if they disagree, then more information is needed to determine exactly whether or not that should be called different species. Debates about taxonomy are ongoing and are likely going to be relevant for years to come, but form critical components of understanding biodiversity, patterns of evolution, and creating effective conservation legislation to protect endangered or threatened species (for whichever groups we decide are species).
Emotion and spirituality are concepts that inherently seem at odds with the fundamentally stoic, empirical nature of scientific research. Science is based on a rigorous system of objectivity, repeatability and empiricism that, at face value, appears to completely disregard subjective aspects such as emotion, spirituality or religion. But in the same way that this drives the division of art from science, removing these subjective components of science can take away some of the personal significance and driving factors of scientific discipline.
Emotions as a driving force in science
For many scientists, emotional responses to inquiry, curiosity and connection are important components of their initial drive to study science in the first place. The natural curiosity of humanity, the absolute desire to know and understand the world around us, is fundamental to scientific advancement (and is a likely source of science as a concept in the first place). We care deeply about understanding many aspects of the natural world, and for many there is a strong emotional connection to our study fields. Scientists are fundamentally drawn to this career path based on some kind of emotional desire to better understand it.
Although it’s likely a massive cliché, Contactis one of my favourite science-fiction movies for simultaneously tackling faith, emotion, rationality, and scientific progress. And no doubt any literary student could dissect these various themes over and over and discuss exactly how the movie balances the opposing concepts of faith in the divine and scientific inquiry (and the overlap of the two). But for me, the most heartfelt aspect the movie is the portrayal of Ellie Arroway: a person who is insatiably driven to science, to the point of sacrificing many things in her life (including faith). But she’s innately an emotional person; when her perspectives are challenged by her observations, it’s a profound moment for her as a person. Ellie, to me, represents scientists pretty well: passionate, driven, idealistic but rational and objective as best as she can be. These traits make her very admirable (and a great protagonist, as far as I’m concerned).
I would not, under ordinary circumstances, consider myself to be particularly sentimental or spiritual. I don’t believe in many spiritual concepts (including theism, the afterlife, or concepts of a ‘soul’), and try to handle life as rationally and objectively as I can (sometimes not very successful given my mental health). But I can’t even remotely deny that there is a strong emotional or spiritual attachment to my field of science. Without delving too much into my own personal narrative (at the risk of being a little self-absorbed and pretentious; it’s also been covered a little in another post), the emotional connection I share with the life of Earth is definitely something that drove me to study biology and evolution. The sense of wonder and curiosity at observing the myriad of creatures and natural selection can concoct. The shared feeling of being alive in all of its aspects. The mystery of the world being seen through eyes very different to ours.
Although it’s of course always better to frame an argument or present research in an objective, rational matter, people have a tendency to respond well to appeal to emotion. In this sense, presenting scientific research as something that can be evocative, powerful and emotional is, in my belief, a good tactic to get the general public invested in science. Getting people to care about our research, our study species, and our findings is a difficult task but one that is absolutely necessary for the longevity and development of science at both the national and global level.
Pretending the science is emotionless and apathetic is counterproductive to the very things that drove us to do the science in the first place. Although we should attempt to be aware of, and distance, our emotions from the objective, data-based analysis of our research, admitting and demonstrating our passions (and why we feel so passionate) is critical in distilling science into the general population. Science should be done rationally and objectively but driven by emotional characteristics such as wonder, curiosity and fascination.
But the real question is: why are there so many endemics in Australia? What is so special about our country that lends to our unique flora and fauna? Although we naturally associate tropical regions with lush, vibrant and diverse life, most of Australia is complete desert. That said, most of our species are concentrated in the tropical regions of the country, particularly in the upper east coast and far north (the ‘Top End’).
There are a number of different factors which contribute to the high species diversity of Australia. Most notably is how isolated we are as a continent: Australia has been separated from most of the rest of the world for millions of years. In this time, the climate has varied dramatically as the island shifted northward, creating a variety of changing environments and unique ecological niches for species to specialise into. We refer to these species groups as ‘Gondwana relicts’, since their last ancestor with the rest of the world would have been distributed across the supercontinent Gondwana over 100 million years ago. These include marsupials, many birds groups (including ratites and megapodes), many fish groups and a plethora of others. A Gondwanan origin explains why they are only found within Australia, southern Africa and South America (the closest landmass that was also historically connected to Gondwana).
Early arrivals and naturalisation to the Australian ecosystem
Eventually, this connection also brought with them one of our most iconic species; the dingo. Estimates of their arrival dates the migration at around 6 thousand years ago. As Australia’s only ‘native’ dog, there has been much debate about its status as an Australian icon. To call the dingo ‘native’ implies it’s always been there: but 6 thousand years is more than enough time to become ingrained within the ecosystem in a stable fashion. So, to balance the debate (and prevent the dingo from being labelled as an ‘invasive pest’ unfairly), we often refer to them as ‘naturalised’. This term helps us to disentangle modern-day pests, many of which our immensely destructive to the natural environment, from other species that have naturally migrated and integrated many years ago.
Invaders of the Australian continent
Of course, we can never ignore the direct impacts of humans on the ecosystem. Particularly with European settlement, another plethora of animals were introduced for the first time into Australia; these were predominantly livestock animals or hunting-related species (both as predators and prey). This includes the cane toad, widely regarded as one of the biggest errors in pest control on the planet.
When European settlers in the 1930s attempted to grow sugar cane in the far eastern part of the country, they found their crops decimated by a local beetle. In an effort to eradicate them, they brought over a species of cane toad, with the idea that they would control the beetle population and all would be well. Only, cane toads are particularly lazy and instead of targeting the cane beetles, they just thrived on all the other native invertebrates around. They’re also very resilient and adaptable (and highly toxic), so their numbers exploded and they’ve since spread across a large swathe of the country. Their toxic skin makes them fatal food objects for many native predators and they strongly compete against other similar native animals (such as our own amphibians). The cane toad introduction of 1935 is the poster child of how bad failed pest control can be.
But is native always better?
History tells a very stark tale about the poor native animals and the ravenous, rampaging pest species. Because of this, it is a widely adopted philosophical viewpoint that ‘native is always best’. And while I don’t disagree with the sentiment (of course we need to preserve our native wildlife, and not the massively overabundant pests), there are rare examples where nature is a little more complicated. In Australia, this is exemplified in the noisy miner.
The noisy miner is a small bird which, much like its name implies, is incredibly noisy and aggressive. It’s highly abundant, found predominantly throughout urban and suburban areas, and seems to dominate the habitat. It does this by bullying out other bird species from nesting grounds, creating a monopoly on the resource to the exclusion of many other species (even larger ones such as crows and magpies). Despite being native, it seems to have thrived on human alteration of the landscape and is a serious threat to the survival and longevity of many other species. If we thought of it solely under the ‘nature is best’ paradigm, we would dismiss the noisy miner as ‘doing what it should be.’ The truth is really more of a philosophical debate: is it natural to let the noisy miner outcompete many other natives, possibly resulting in their extinction? Or is it only because of human interference (and thus is our responsibility to fix) that the noisy miner is doing so well in the first place? It’s not a simple question to answer, although the latter seems to be incredibly important.
The amazing biodiversity of Australia is a badge of honour we should wear with patriotic pride. Conservation efforts of our endemic fauna are severely limited by a lack of funding and resources, and despite a general acceptance of the importance of diverse ecosystems we remain relatively ineffective at preserving it. Understanding and connecting with our native wildlife, whilst finding methods to control invasive species, is key to conserving our wonderful ecosystems.